some random thoughts and quotes about organised (and disorganised) science

Thursday, 19 November 2009

not just drug design

Drug Design: Cutting Edge Approaches, published in 2002, is a collection of highly enlightening reviews, even if some of the approaches may be not so cutting-edgey any longer. (Really, one should never name a book like that.) The two chapters authored by Darren Flower (who is also an editor of the book) are a pleasure to read, not least because they put the drug design into fascinating historical and philosophical context.

‘Show me a drug without side effects and you are showing me a placebo,’ a former chair of the UK’s committee on drug safety once commented. As pharmaceutical products, of which Viagra is the clearest example, are treated more and more as part of a patient’s lifestyle, the importance of side effects is likely to grow. A recent study concluded that over 2 million Americans become seriously ill every year, and over 100,000 actually die, because of adverse reactions to prescribed medications.

On bioinformatics:

Academic bioinformaticians sometimes seem to lose sight of their place as an intermediate taking, interpreting, and ultimately returning data from one experimental scientist to another. There is a need for bioinformatics to keep in close touch with wet lab biologists, servicing and supporting their needs, either directly or indirectly, rather than becoming obsessed with their own recondite or self referential concerns.

On molecular similarity:

There is, ultimately, no ‘gold standard’ by which to judge the performance of different similarity measures. There is no consensus between chemists, or computer algorithms, and there isn’t one between receptors either. There is no universally applicable definition of chemical diversity, only local, context-dependent ones. The only correct set of rules would be those that a receptor chooses to select molecules: but these will vary greatly between different receptors. This has not discouraged the development of a large literature — comparing methods, primarily in the context of justifying the apparent superiority of a method that the authors have developed; these are often large, complex, yet discombobulatingly terse papers which assaults the reader with the weight of information rather than the arguments of sweet reason.

From Computational vaccine design:

Death, the pale horseman, comes in many guises, covering diverse causes from individual natural disasters to accidental injury. Natural disasters, or what insurance brokers are pleased to call acts of god, would figure highly on the average individual’s list of greatest causes of death and destruction.

One of the most significant events in the history of human disease interaction was the new world holocaust that affected South America in the century or so after its ‘discovery’ by the Spanish. <...> The catastrophic decline in the indigenous Indian population was on a scale unmatched even in the 20th century, and was likely to have been the greatest ever loss of an aboriginal population.